Avogadro-Discuss Digest, Vol 28, Issue 4

Dear Geoff, Dear Avogadro Forum,

Sorry that I was not clear in my question. I want to model the
ferroelectric behavior in the croconic acid and its FTIR. I want to
publish using avogadro and for this collaborations are very welcome.
Additionally to that I have a crash in the avogadro 1.0.3.

Thanks a lot,

Alex

Problem signature:
Problem Event Name: APPCRASH
Application Name: avogadro.exe
Application Version: 0.0.0.0
Application Timestamp: 4db4b9a7
Fault Module Name: openbabel-2.dll
Fault Module Version: 0.0.0.0
Fault Module Timestamp: 4db1fa94
Exception Code: c0000005
Exception Offset: 00006414
OS Version: 6.0.6002.2.2.0.768.3
Locale ID: 1033
Additional Information 1: fd00
Additional Information 2: ea6f5fe8924aaa756324d57f87834160
Additional Information 3: fd00
Additional Information 4: ea6f5fe8924aaa756324d57f87834160

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On 25 November 2011 18:09,
avogadro-discuss-request@lists.sourceforge.net wrote:

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Today’s Topics:

  1. Re: problems to visualize molecules (Geoff Hutchison)
  2. Drawing from GAMESS (g_sanjurjo@hotmail.com)
  3. Re: [SPAM] Drawing from GAMESS (Jan Halborg Jensen)
  4. Re: Avogadro-Discuss Digest, Vol 28, Issue 3 (Alejandro Heredia)
  5. atomic charges on each atom (Victor Eduardo Bahamonde Padilla)
  6. Re: atomic charges on each atom (David Lonie)

Message: 1
Date: Fri, 18 Nov 2011 16:22:51 -0500
From: Geoff Hutchison geoff.hutchison@gmail.com
Subject: Re: [Avogadro-Discuss] problems to visualize molecules
To: avogadro-discuss@lists.sourceforge.net
Message-ID: 2A33FA94-BB71-4A67-B7AD-7660A6831AA7@geoffhutchison.net
Content-Type: text/plain; charset=iso-8859-1

QStackedLayout::setCurrentWidget: Widget 0x18d3750 not contained in stack
libpng warning: Ignoring attempt to set cHRM RGB triangle with zero area
Gtk-Message: (for origin information, set GTK_DEBUG): failed to retrieve property GtkWidget::visited-link-color' of typeGdkColor’ from rc file value “((GString*) 0x24b22e0)” of type `GString’

There are warning messages, but not indicators of errors. I suspect that upgrading has given you a lousy OpenGL driver. These types of artifacts are typical of driver issues on Windows and Linux.

-Geoff


Message: 2
Date: Mon, 21 Nov 2011 14:31:45 +0100
From: g_sanjurjo@hotmail.com g_sanjurjo@hotmail.com
Subject: [Avogadro-Discuss] Drawing from GAMESS
To: avogadro-discuss@lists.sourceforge.net
Message-ID: BLU0-SMTP19753B8BDD505B09DFE7262E3CB0@phx.gbl
Content-Type: text/plain; charset=“utf-8”

Good morning,

How can I draw molecular densities from GAMESS output?

Thanks


@@@@@@@@@@@@@@@@@@@@@
“It is said that mathematics is the language of nature. If so, then physics is its poetry”

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Message: 3
Date: Mon, 21 Nov 2011 13:47:27 +0000
From: Jan Halborg Jensen jhjensen@chem.ku.dk
Subject: Re: [Avogadro-Discuss] [SPAM] Drawing from GAMESS
To: "avogadro-discuss@lists.sourceforge.net"
avogadro-discuss@lists.sourceforge.net
Message-ID: 16BDEC8B-BC95-43A4-9F58-5112B352DA8B@ku.dk
Content-Type: text/plain; charset=“us-ascii”

Here is a short description:
http://molecularmodelingbasics.blogspot.com/2009/11/electron-density-reloaded.html

Best regards, Jan
=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-
Jan H. Jensen Professor
Department of Chemistry jhjensen@chem.ku.dk NEW
University of Copenhagen Phone: +45 35 32 02 39
Universitetsparken 5 FAX: +45 35 32 02 14
2100 Copenhagen Denmark
http://tinyurl.com/jhjensen
http://molecularmodelingbasics.blogspot.com
http://proteinsandwavefunctions.blogspot.com/
=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-

On Nov 21, 2011, at 2:31 PM, g_sanjurjo@hotmail.com wrote:

Good morning,

How can I draw molecular densities from GAMESS output?

Thanks


@@@@@@@@@@@@@@@@@@@@@
“It is said that mathematics is the language of nature. If so, then physics is its poetry”


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Message: 4
Date: Tue, 22 Nov 2011 12:49:59 +0000
From: Alejandro Heredia alejandropicoheredia@googlemail.com
Subject: Re: [Avogadro-Discuss] Avogadro-Discuss Digest, Vol 28, Issue
3
To: avogadro-discuss@lists.sourceforge.net, geoff.hutchison@gmail.com
Message-ID:
CAMOwbg=-akg+EOoCgeyP0bCtDvzNpckSN9N8YoWUuYbRHo4tbQ@mail.gmail.com
Content-Type: text/plain; charset=ISO-8859-1

Dear Geoff,

Thanks a lot for you help and your patience. Im very sorry for my
delay in this mail. I would like to know if possible to see the
ferroelectric behavior of 1, 2, n molecules up to form a unit cell.
One example of what I would like to model is the croconic acid
(Horiuchi) in just one molecule and “apply” an electric field and the
same with the crystal unit cell. I know for instance HyperChem can do
this easily. I would like to try Avogadro or other free software (I
accept kind suggestions :wink: ). In the other hand, about the mineralogy
of polymorphs I work with biominerals and FTIR. For the model Im
interested in CaCO3 in shells (aragonite, calcite) and in this case, I
would like to know the environment when a molecule “feels” the most
stable conformation. I mean, beginning from one molecule of CaCO3 up
to the formation of the CaCO3 polymorph unit cell. I would like to
develop this two ideas by using Avogadro…having a difficulty. Nobody
in my environment works with modeling and I just used HyperChem
before. Anyhow Im always very glad to know new methods and suggestions
as to publish nice results.

Kindest Regards,

Alex

(Horiuchi) http://www.physorg.com/wire-news/29836312/discovery-of-ferroelectricity-of-croconic-acid-a-low-molecular-w.html

Message: 7
Date: Wed, 02 Nov 2011 10:28:09 -0400
From: Geoff Hutchison geoff.hutchison@gmail.com
Subject: Re: [Avogadro-Discuss] Electric field and stability of a unit
cell
To: avogadro-discuss@lists.sourceforge.net
Message-ID: 3FBD9C93-48F9-4513-A4DF-A858CD3ED918@geoffhutchison.net
Content-Type: text/plain; charset=us-ascii

Dear Alex,

My name is Alejandro Heredia Barbero and I try to measure the effect
of an electric field in organic molecules.

I’m not quite sure what you mean here. There are many possible effects
of an electric field on an organic molecule – not the least of which
is a change in the electron density due to polarizability (and
non-linear effects).

Most of these effects are best treated with various quantum chemistry
packages, like MOPAC or Gaussian. (Although not all quantum packages
can treat electric fields.)

This is one area of my research, so if you can be a bit more specific,
I’m sure we can help you.

this. Additionally to this, I would like to do an insight in stability
of molecules when are in polymorphs. Your help would be very important
for my professional activities.

Again, I’m not sure I completely understand what you wish to learn. Do
you wish to find different polymorphs for a given compound? Or do you
have different polymorph crystal structures and you wish to calculate
which is the most stable form?

The latter is definitely easier, but also requires a quantum package,
for example ABINIT or VASP.

Hope that helps,
-Geoff

On 17 November 2011 17:18,
avogadro-discuss-request@lists.sourceforge.net wrote:

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Today’s Topics:

? 1. Re: Status of PyQt signals (Noel O’Boyle)
? 2. problems to visualize molecules (leonardo espinosa)


Message: 1
Date: Thu, 17 Nov 2011 17:10:48 +0100
From: “Noel O’Boyle” baoilleach@gmail.com
Subject: Re: [Avogadro-Discuss] Status of PyQt signals
To: avogadro-discuss@lists.sourceforge.net
Message-ID:
? ? ? ?CAOC-GK22J8yV309m=wFOYW4LVqK-hahGusWXQMS_3LBaaP42bQ@mail.gmail.com
Content-Type: text/plain; charset=ISO-8859-1

Actually it seems to be working now :slight_smile: My only problem is that I
can’t figure out exactly why it was failing before…

  • Noel

On 17 November 2011 15:55, Noel O’Boyle baoilleach@gmail.com wrote:

Hi all,

I’ve been successfully usnig basic Signals from PyQt (Avo 1.0.1+Python
on Windows) but I’m ready to throw in the towel on using signals with
parameters:

I have a QTableWidget and am trying to catch the signal when someone
clicks on a cell:

? ?QObject.connect(self.allpharmas,
? ? ? ? ? ? ? ? ? ?SIGNAL(“currentCellChanged(int, int, int, int)”),
? ? ? ? ? ? ? ? ? ?self, SLOT(“selectPharmacophore(int,int,int,int)”))

The signal never arrives at selectPharmacophore:
?@pyqtSignature(“int,int,int,int”)
?def selectPharmacophore(self, a, b, c, d):
? ?self.debug(“select pharmacophore”)

Does anyone know whether I am doing something wrong here? If these
signals aren’t usable it really limits the possibilities of extending
Avo through Python.

  • Noel

Message: 2
Date: Thu, 17 Nov 2011 17:00:42 +0100
From: leonardo espinosa leonardo.espinosa@csic.es
Subject: [Avogadro-Discuss] problems to visualize molecules
To: avogadro-discuss@lists.sourceforge.net
Message-ID:
? ? ? ?CACqbX0Z5RNdo3OyEQoNVf1VsnNG7KimBmBmfBBqsTTJjJXrsaw@mail.gmail.com
Content-Type: text/plain; charset=“iso-8859-1”

Dear avogadro users,

I’ve been using avogadro since a couple of months ago, it worked perfectly
on the last Ubuntu versions (10.04 and 10.10),
a couple of weeks ago I upgrade to 11.04 and since this I have problems
opening xyz and pdb files, I attached you a
snapshot of the screen and the terminal message:

QStackedLayout::setCurrentWidget: Widget 0x18d3750 not contained in stack
libpng warning: Ignoring attempt to set cHRM RGB triangle with zero area
Gtk-Message: (for origin information, set GTK_DEBUG): failed to retrieve
property GtkWidget::visited-link-color' of typeGdkColor’ from rc file
value “((GString*) 0x24b22e0)” of type `GString’

All the best,

Leonardo Andr?s Espinosa Leal
PhD student of PNAM (Physics of Nanostructures and Advanced Materials)
Nano-Bio Spectroscopy Group (web: http://nano-bio.ehu.es/)
University of the Basque Country / Euskal Herriko Unibertsitatea (UPV/EHU)
Materials Physics Center (http://cfm.ehu.es/)
Donostia-San Sebasti?n, Gip?zkoa (Spain)


European Theoretical Spectroscopy Facility (ETSF), Spanish node
web: http://www.etsf.es/
Joxe Mari Korta building, Av. de Tolosa, 72, 20018. ETSF rooms
Donostia-San Sebasti?n, Gipuzkoa (Spain).


Contact:
Phone: +34 943018820 ? ? ? ? ? ? ? Fax: +34 943018390
Mobile:+34 655731411
alternative emails:
email1: laespinosa001 [at] ikasle [dot] ehu [dot] es
email2: espinosa [dot] leal [at] gmail [dot] com
skype: espinosa [dot] leal

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End of Avogadro-Discuss Digest, Vol 28, Issue 3



Message: 5
Date: Fri, 25 Nov 2011 10:46:21 -0300
From: Victor Eduardo Bahamonde Padilla victorb@live.cl
Subject: [Avogadro-Discuss] atomic charges on each atom
To: avogadro-mail-list avogadro-discuss@lists.sourceforge.net
Message-ID: BAY156-W2606F9A558DBC23E8D3041BACF0@phx.gbl
Content-Type: text/plain; charset=“iso-8859-1”

Hello
Is there any way to see the value of the atomic charges on each atom of the molecule displayed as gaussview?

Thanks in advance

V?ctor E. Bahamonde Padilla
Laboratorio Fisicoquimica Molecular
Departamento de Qu?mica
Facultad de Ciencias
Universidad de Chile
Phone: 562-978-7443
veduardo@ug.uchile.cl

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Message: 6
Date: Fri, 25 Nov 2011 13:09:03 -0500
From: David Lonie loniedavid@gmail.com
Subject: Re: [Avogadro-Discuss] atomic charges on each atom
To: avogadro-discuss@lists.sourceforge.net
Message-ID:
CABzw8w9rasJWSUSKnCGakrCV7efST91qLvkpbZOs7Lje6LhGzw@mail.gmail.com
Content-Type: text/plain; charset=ISO-8859-1

On Fri, Nov 25, 2011 at 8:46 AM, Victor Eduardo Bahamonde Padilla
victorb@live.cl wrote:

Hello
Is there any way to see the value of the atomic charges on each atom of the
molecule displayed as gaussview?

Click “Display Settings” and check “Label”, then open the label
configuration dialog. In Atom Labels --> Text there are Formal Charge
and Partial Charge options. However, I don’t see an way to set the
formal charges, other than to read them in from a calculation or enter
them manually under View --> Properties --> Atom Properties.

Does anyone know of a way to perceive them? This sounds like something
OpenBabel should be able do.

Dave



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security threats, fraudulent activity, and more. Splunk takes this
data and makes sense of it. IT sense. And common sense.
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End of Avogadro-Discuss Digest, Vol 28, Issue 4